/*----------------------------------------------------------------------------
* Name: h5rcreate_region_c
* Purpose: Call H5Rcreate to create a reference to dataset region
* region
* Inputs: loc_id - file or group identifier
* name - name of the dataset
* namelen - name length
* space_id - dataset space identifier
* Outputs: ref - reference to the dataset region
* Returns: 0 on success, -1 on failure
* Programmer: Elena Pourmal
* Wednesday, December 1, 1999
* Modifications:
*---------------------------------------------------------------------------*/
int_f
nh5rcreate_region_c (int_f *ref, hid_t_f *loc_id, _fcd name, int_f *namelen, hid_t_f *space_id)
{
int ret_value = -1;
hid_t c_loc_id;
hid_t c_space_id;
int ret_value_c;
char *c_name;
int c_namelen;
hdset_reg_ref_t ref_c;
/*
* Convert FORTRAN name to C name
*/
c_namelen = *namelen;
c_name = (char *)HD5f2cstring(name, c_namelen);
if (c_name == NULL) return ret_value;
/*
* Call H5Rcreate function.
*/
c_loc_id = *loc_id;
c_space_id = *space_id;
ret_value_c = H5Rcreate(&ref_c, c_loc_id, c_name, H5R_DATASET_REGION, c_space_id);
HDfree(c_name);
if (ret_value_c >= 0) {
HDmemcpy (ref, &ref_c, H5R_DSET_REG_REF_BUF_SIZE);
ret_value = 0;
}
return ret_value;
}
/*----------------------------------------------------------------------------
* Name: h5rcreate_object_c
* Purpose: Call H5Rcreate to create a reference to an object
* Inputs: loc_id - file or group identifier
* name - name of the dataset
* namelen - name length
* Outputs: ref - reference to the object
* Returns: 0 on success, -1 on failure
* Programmer: Elena Pourmal
* Wednesday, December 1, 1999
* Modifications:
*---------------------------------------------------------------------------*/
int_f
nh5rcreate_object_c (haddr_t_f *ref, hid_t_f *loc_id, _fcd name, int_f *namelen)
{
int ret_value = -1;
hid_t c_loc_id;
int ret_value_c;
char *c_name;
int c_namelen;
hobj_ref_t ref_c;
/*
* Convert FORTRAN name to C name
*/
c_namelen = *namelen;
c_name = (char *)HD5f2cstring(name, c_namelen);
if (c_name == NULL) return ret_value;
/*
* Call H5Rcreate function.
*/
c_loc_id = *loc_id;
ret_value_c = H5Rcreate(&ref_c, c_loc_id, c_name, H5R_OBJECT, -1);
HDfree(c_name);
if (ret_value_c >= 0) {
*ref=(haddr_t_f)ref_c;
ret_value = 0;
}
return ret_value;
}
void DCDataSet::createReference(hid_t refGroup,
hid_t srcGroup,
DCDataSet &srcDataSet)
throw (DCException)
{
if (opened)
throw DCException(getExceptionString("createReference: dataset is already open"));
if (checkExistence && H5Lexists(refGroup, name.c_str(), H5P_LINK_ACCESS_DEFAULT))
throw DCException(getExceptionString("createReference: this reference already exists"));
getLogicalSize().set(srcDataSet.getLogicalSize());
this->ndims = srcDataSet.getNDims();
if (H5Rcreate(®ionRef, srcGroup, srcDataSet.getName().c_str(), H5R_OBJECT, -1) < 0)
throw DCException(getExceptionString("createReference: failed to create region reference"));
hsize_t ndims = 1;
dataspace = H5Screate_simple(1, &ndims, NULL);
if (dataspace < 0)
throw DCException(getExceptionString("createReference: failed to create dataspace for reference"));
dataset = H5Dcreate(refGroup, name.c_str(), H5T_STD_REF_OBJ,
dataspace, H5P_DEFAULT, dsetProperties, H5P_DEFAULT);
if (dataset < 0)
throw DCException(getExceptionString("createReference: failed to create dataset for reference"));
if (H5Dwrite(dataset, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL,
dsetWriteProperties, ®ionRef) < 0)
throw DCException(getExceptionString("createReference: failed to write reference"));
isReference = true;
opened = true;
}
//--------------------------------------------------------------------------
// Function: H5Object::p_reference (protected)
// Purpose Creates a reference to an HDF5 object or a dataset region.
// Parameters
// name - IN: Name of the object to be referenced
// dataspace - IN: Dataspace with selection
// ref_type - IN: Type of reference; default to \c H5R_DATASET_REGION
// Exception H5::IdComponentException
// Programmer Binh-Minh Ribler - May, 2004
//--------------------------------------------------------------------------
void H5Object::p_reference(void* ref, const char* name, hid_t space_id, H5R_type_t ref_type) const
{
herr_t ret_value = H5Rcreate(ref, getId(), name, ref_type, space_id);
if (ret_value < 0)
{
throw IdComponentException("", "H5Rcreate failed");
}
}
//--------------------------------------------------------------------------
// Function: H5Location::p_reference (protected)
// Purpose Creates a reference to an HDF5 object or a dataset region.
// Parameters
// name - IN: Name of the object to be referenced
// dataspace - IN: Dataspace with selection
// ref_type - IN: Type of reference; default to \c H5R_DATASET_REGION
// Exception H5::ReferenceException
// Programmer Binh-Minh Ribler - May, 2004
//--------------------------------------------------------------------------
void H5Location::p_reference(void* ref, const char* name, hid_t space_id, H5R_type_t ref_type) const
{
herr_t ret_value = H5Rcreate(ref, getId(), name, ref_type, space_id);
if (ret_value < 0)
{
throw ReferenceException(inMemFunc("reference"), "H5Rcreate failed");
}
}
void NSDFWriter::createEventMap()
{
herr_t status;
hid_t eventMapContainer = require_group(filehandle_, MAPEVENTSRC);
// Open the container for the event maps
// Create the Datasets themselves (one for each field - each row
// for one object).
for (map< string, vector < string > >::iterator ii = classFieldToEventSrc_.begin();
ii != classFieldToEventSrc_.end();
++ii){
vector < string > pathTokens;
tokenize(ii->first, "/", pathTokens);
string className = pathTokens[0];
string fieldName = pathTokens[1];
hid_t classGroup = require_group(eventMapContainer, className);
hid_t strtype = H5Tcopy(H5T_C_S1);
status = H5Tset_size(strtype, H5T_VARIABLE);
// create file space
hid_t ftype = H5Tcreate(H5T_COMPOUND, sizeof(hvl_t) +sizeof(hobj_ref_t));
status = H5Tinsert(ftype, "source", 0, strtype);
status = H5Tinsert(ftype, "data", sizeof(hvl_t), H5T_STD_REF_OBJ);
hsize_t dims[1] = {ii->second.size()};
hid_t space = H5Screate_simple(1, dims, NULL);
// The dataset for mapping is named after the field
hid_t ds = H5Dcreate2(classGroup, fieldName.c_str(), ftype, space,
H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
status = H5Sclose(space);
map_type * buf = (map_type*)calloc(ii->second.size(), sizeof(map_type));
// Populate the buffer entries with source uid and data
// reference
for (unsigned int jj = 0; jj < ii->second.size(); ++jj){
buf->source = ii->second[jj].c_str();
char * dsname = (char*)calloc(256, sizeof(char));
ssize_t size = H5Iget_name(classFieldToEvent_[ii->first][jj], dsname, 255);
if (size > 255){
free(dsname);
dsname = (char*)calloc(size, sizeof(char));
size = H5Iget_name(classFieldToEvent_[ii->first][jj], dsname, 255);
}
status = H5Rcreate(&(buf->data), filehandle_, dsname, H5R_OBJECT, -1);
free(dsname);
assert(status >= 0);
}
// create memory space
hid_t memtype = H5Tcreate(H5T_COMPOUND, sizeof(map_type));
status = H5Tinsert(memtype, "source",
HOFFSET(map_type, source), strtype);
status = H5Tinsert(memtype, "data",
HOFFSET(map_type, data), H5T_STD_REF_OBJ);
status = H5Dwrite(ds, memtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
free(buf);
status = H5Tclose(strtype);
status = H5Tclose(ftype);
status = H5Tclose(memtype);
status = H5Dclose(ds);
}
}
/*
* Class: hdf_hdf5lib_H5
* Method: H5Rcreate
* Signature: ([BJLjava/lang/String;IJ)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Rcreate(JNIEnv *env, jclass clss, jbyteArray ref, jlong loc_id, jstring name, jint ref_type, jlong space_id)
{
const char *rName;
herr_t status = -1;
jbyte *refP;
jboolean isCopy2;
PIN_JAVA_STRING(name, rName, -1);
if (ref == NULL) {
UNPIN_JAVA_STRING(name, rName);
h5nullArgument( env, "H5Rcreate: ref is NULL");
} /* end if */
else {
if ((ref_type == H5R_OBJECT) && ENVPTR->GetArrayLength(ENVPAR ref) != H5R_OBJ_REF_BUF_SIZE) {
UNPIN_JAVA_STRING(name, rName);
h5badArgument( env, "H5Rcreate: ref input array != H5R_OBJ_REF_BUF_SIZE");
} /* end if */
else if ((ref_type == H5R_DATASET_REGION) && ENVPTR->GetArrayLength(ENVPAR ref) != H5R_DSET_REG_REF_BUF_SIZE) {
UNPIN_JAVA_STRING(name, rName);
h5badArgument( env, "H5Rcreate: region ref input array != H5R_DSET_REG_REF_BUF_SIZE");
} /* end else if */
else if ((ref_type != H5R_OBJECT) && (ref_type != H5R_DATASET_REGION)) {
UNPIN_JAVA_STRING(name, rName);
h5badArgument( env, "H5Rcreate: ref_type unknown type ");
} /* end else if */
else {
refP = (jbyte*)ENVPTR->GetByteArrayElements(ENVPAR ref, &isCopy2);
if (refP == NULL) {
UNPIN_JAVA_STRING(name, rName);
h5JNIFatalError(env, "H5Rcreate: ref not pinned");
} /* end if */
else {
status = H5Rcreate(refP, (hid_t)loc_id, rName, (H5R_type_t)ref_type, (hid_t)space_id);
UNPIN_JAVA_STRING(name, rName);
if (status < 0) {
ENVPTR->ReleaseByteArrayElements(ENVPAR ref, refP, JNI_ABORT);
h5libraryError(env);
} /* end if */
else {
ENVPTR->ReleaseByteArrayElements(ENVPAR ref, refP, 0);
} /* end else */
} /* end else */
} /* end else */
} /* end else */
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Rcreate */
void DCDataSet::createReference(hid_t refGroup,
hid_t srcGroup,
DCDataSet &srcDataSet,
Dimensions count,
Dimensions offset,
Dimensions stride)
throw (DCException)
{
if (opened)
throw DCException(getExceptionString("createReference: dataset is already open"));
if (checkExistence && H5Lexists(refGroup, name.c_str(), H5P_LINK_ACCESS_DEFAULT))
throw DCException(getExceptionString("createReference: this reference already exists"));
getLogicalSize().set(count);
this->ndims = srcDataSet.getNDims();
count.swapDims(this->ndims);
offset.swapDims(this->ndims);
stride.swapDims(this->ndims);
// select region hyperslab in source dataset
if (H5Sselect_hyperslab(srcDataSet.getDataSpace(), H5S_SELECT_SET,
offset.getPointer(), stride.getPointer(),
count.getPointer(), NULL) < 0 ||
H5Sselect_valid(srcDataSet.getDataSpace()) <= 0)
throw DCException(getExceptionString("createReference: failed to select hyperslap for reference"));
if (H5Rcreate(®ionRef, srcGroup, srcDataSet.getName().c_str(), H5R_DATASET_REGION,
srcDataSet.getDataSpace()) < 0)
throw DCException(getExceptionString("createReference: failed to create region reference"));
hsize_t ndims = 1;
dataspace = H5Screate_simple(1, &ndims, NULL);
if (dataspace < 0)
throw DCException(getExceptionString("createReference: failed to create dataspace for reference"));
dataset = H5Dcreate(refGroup, name.c_str(), H5T_STD_REF_DSETREG,
dataspace, H5P_DEFAULT, dsetProperties, H5P_DEFAULT);
if (dataset < 0)
throw DCException(getExceptionString("createReference: failed to create dataset for reference"));
if (H5Dwrite(dataset, H5T_STD_REF_DSETREG, H5S_ALL, H5S_ALL,
dsetWriteProperties, ®ionRef) < 0)
throw DCException(getExceptionString("createReference: failed to write reference"));
isReference = true;
opened = true;
}
int main(void)
{
hid_t file_id; /* file identifier */
hid_t space_id; /* dataspace identifiers */
hid_t spacer_id;
hid_t dsetv_id; /*dataset identifiers*/
hid_t dsetr_id;
hsize_t dims[2] = {2,9};
hsize_t dimsr[1] = {2};
int rank = 2;
int rankr =1;
herr_t status;
hdset_reg_ref_t ref[2];
hdset_reg_ref_t ref_out[2];
int data[2][9] = {{1,1,2,3,3,4,5,5,6},{1,2,2,3,4,4,5,6,6}};
int data_out[2][9] = {{0,0,0,0,0,0,0,0,0},{0,0,0,0,0,0,0,0,0}};
hsize_t start[2];
hsize_t count[2];
hsize_t coord[2][3] = {{0, 0, 1}, {6, 0, 8}};
unsigned num_points = 3;
int i, j;
size_t name_size1, name_size2;
char buf1[10], buf2[10];
/*
* Create file with default file access and file creation properties.
*/
file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create dataspace for datasets.
*/
space_id = H5Screate_simple(rank, dims, NULL);
spacer_id = H5Screate_simple(rankr, dimsr, NULL);
/*
* Create integer dataset.
*/
dsetv_id = H5Dcreate2(file_id, dsetnamev, H5T_NATIVE_INT, space_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
/*
* Write data to the dataset.
*/
status = H5Dwrite(dsetv_id, H5T_NATIVE_INT, H5S_ALL , H5S_ALL, H5P_DEFAULT,data);
status = H5Dclose(dsetv_id);
/*
* Dataset with references.
*/
dsetr_id = H5Dcreate2(file_id, dsetnamer, H5T_STD_REF_DSETREG, spacer_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create a reference to the hyperslab.
*/
start[0] = 0;
start[1] = 3;
count[0] = 2;
count[1] = 3;
status = H5Sselect_hyperslab(space_id, H5S_SELECT_SET, start, NULL, count, NULL);
status = H5Rcreate(&ref[0], file_id, dsetnamev, H5R_DATASET_REGION, space_id);
/*
* Create a reference to elements selection.
*/
status = H5Sselect_none(space_id);
status = H5Sselect_elements(space_id, H5S_SELECT_SET, num_points, (const hsize_t *)coord);
status = H5Rcreate(&ref[1], file_id, dsetnamev, H5R_DATASET_REGION, space_id);
/*
* Write dataset with the references.
*/
status = H5Dwrite(dsetr_id, H5T_STD_REF_DSETREG, H5S_ALL, H5S_ALL, H5P_DEFAULT,ref);
/*
* Close all objects.
*/
status = H5Sclose(space_id);
status = H5Sclose(spacer_id);
status = H5Dclose(dsetr_id);
status = H5Fclose(file_id);
/*
* Reopen the file to read selections back.
*/
file_id = H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT);
/*
* Reopen the dataset with object references and read references
* to the buffer.
*/
dsetr_id = H5Dopen2(file_id, dsetnamer, H5P_DEFAULT);
status = H5Dread(dsetr_id, H5T_STD_REF_DSETREG, H5S_ALL, H5S_ALL,
H5P_DEFAULT, ref_out);
/*
* Dereference the first reference.
*/
dsetv_id = H5Rdereference2(dsetr_id, H5P_DEFAULT, H5R_DATASET_REGION, &ref_out[0]);
/*
* Get name of the dataset the first region reference points to
* using H5Rget_name
*/
name_size1 = H5Rget_name(dsetr_id, H5R_DATASET_REGION, &ref_out[0], (char*)buf1, 10);
printf(" Dataset's name (returned by H5Rget_name) the reference points to is %s, name length is %d\n", buf1, (int)name_size1);
/*
* Get name of the dataset the first region reference points to
* using H5Iget_name
*/
name_size2 = H5Iget_name(dsetv_id, (char*)buf2, 10);
printf(" Dataset's name (returned by H5Iget_name) the reference points to is %s, name length is %d\n", buf2, (int)name_size2);
space_id = H5Rget_region(dsetr_id, H5R_DATASET_REGION,&ref_out[0]);
/*
* Read and display hyperslab selection from the dataset.
*/
status = H5Dread(dsetv_id, H5T_NATIVE_INT, H5S_ALL, space_id,
H5P_DEFAULT, data_out);
printf("Selected hyperslab: ");
for (i = 0; i <= 1; i++)
{
printf("\n");
for (j = 0; j <= 8; j++)
printf("%d ", data_out[i][j]);
}
printf("\n");
/*
* Close dataspace and the dataset.
*/
status = H5Sclose(space_id);
status = H5Dclose(dsetv_id);
/*
* Initialize data_out array again to get point selection.
*/
for (i = 0; i <= 1; i++)
for (j = 0; j <= 8; j++)
data_out[i][j] = 0;
/*
* Dereference the second reference.
*/
dsetv_id = H5Rdereference2(dsetr_id, H5P_DEFAULT, H5R_DATASET_REGION, &ref_out[1]);
space_id = H5Rget_region(dsetv_id, H5R_DATASET_REGION,&ref_out[1]);
/*
* Read selected data from the dataset.
*/
status = H5Dread(dsetv_id, H5T_NATIVE_INT, H5S_ALL, space_id,
H5P_DEFAULT, data_out);
printf("Selected points: ");
for (i = 0; i <= 1; i++)
{
printf("\n");
for (j = 0; j <= 8; j++)
printf("%d ", data_out[i][j]);
}
printf("\n");
/*
* Close dataspace and the dataset.
*/
status = H5Sclose(space_id);
status = H5Dclose(dsetv_id);
status = H5Dclose(dsetr_id);
status = H5Fclose(file_id);
return 0;
}
int
main(void) {
hid_t fid; /* File, group, datasets, datatypes */
hid_t gid_a; /* and dataspaces identifiers */
hid_t did_b, sid_b, tid_b;
hid_t did_r, tid_r, sid_r;
H5O_type_t obj_type;
herr_t status;
hobj_ref_t *wbuf; /* buffer to write to disk */
hobj_ref_t *rbuf; /* buffer to read from disk */
hsize_t dim_r[1];
hsize_t dim_b[2];
/*
* Create a file using default properties.
*/
fid = H5Fcreate(H5FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create group "A" in the file.
*/
gid_a = H5Gcreate2(fid, "A", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create dataset "B" in the file.
*/
dim_b[0] = 2;
dim_b[1] = 6;
sid_b = H5Screate_simple(2, dim_b, NULL);
did_b = H5Dcreate2(fid, "B", H5T_NATIVE_FLOAT, sid_b, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create dataset "R" to store references to the objects "A" and "B".
*/
dim_r[0] = 2;
sid_r = H5Screate_simple(1, dim_r, NULL);
tid_r = H5Tcopy(H5T_STD_REF_OBJ);
did_r = H5Dcreate2(fid, "R", tid_r, sid_r, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
/*
* Allocate write and read buffers.
*/
wbuf = (hobj_ref_t *)malloc(sizeof(hobj_ref_t) * 2);
rbuf = (hobj_ref_t *)malloc(sizeof(hobj_ref_t) * 2);
/*
* Create references to the group "A" and dataset "B"
* and store them in the wbuf.
*/
H5Rcreate(&wbuf[0], fid, "A", H5R_OBJECT, (hid_t)-1);
H5Rcreate(&wbuf[1], fid, "B", H5R_OBJECT, (hid_t)-1);
/*
* Write dataset R using default transfer properties.
*/
status = H5Dwrite(did_r, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, wbuf);
/*
* Close all objects.
*/
H5Gclose(gid_a);
H5Sclose(sid_b);
H5Dclose(did_b);
H5Tclose(tid_r);
H5Sclose(sid_r);
H5Dclose(did_r);
H5Fclose(fid);
/*
* Reopen the file.
*/
fid = H5Fopen(H5FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT);
/*
* Open and read dataset "R".
*/
did_r = H5Dopen2(fid, "R", H5P_DEFAULT);
status = H5Dread(did_r, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, rbuf);
/*
* Find the type of referenced objects.
*/
status = H5Rget_obj_type2(did_r, H5R_OBJECT, &rbuf[0], &obj_type);
if(obj_type == H5O_TYPE_GROUP)
printf("First dereferenced object is a group. \n");
status = H5Rget_obj_type2(did_r, H5R_OBJECT, &rbuf[1], &obj_type);
if(obj_type == H5O_TYPE_DATASET)
printf("Second dereferenced object is a dataset. \n");
/*
* Get datatype of the dataset "B"
*/
did_b = H5Rdereference2(did_r, H5P_DEFAULT, H5R_OBJECT, &rbuf[1]);
tid_b = H5Dget_type(did_b);
if(H5Tequal(tid_b, H5T_NATIVE_FLOAT))
printf("Datatype of the dataset is H5T_NATIVE_FLOAT.\n");
printf("\n");
/*
* Close all objects and free memory buffers.
*/
H5Dclose(did_r);
H5Dclose(did_b);
H5Tclose(tid_b);
H5Fclose(fid);
free(rbuf);
free(wbuf);
return 0;
}
/*****************************************************************************
This function generates attributes, groups, and datasets of many types.
Parameters:
fname: file_name.
ngrps: number of top level groups.
ndsets: number of datasets.
attrs: number of attributes.
nrow: number of rows in a dataset.
chunk: chunk size (single number).
vlen: max vlen size.
comp: use latest format.
latest: use gzip comnpression.
Return: Non-negative on success/Negative on failure
Programmer: Peter Cao <*****@*****.**>, Jan. 2013
****************************************************************************/
herr_t create_perf_test_file(const char *fname, int ngrps, int ndsets,
int nattrs, hsize_t nrows, hsize_t dim0, hsize_t chunk, int vlen,
int compressed, int latest)
{
int i, j, k;
hid_t fid, sid_null, sid_scalar, sid_1d, sid_2d, did, aid, sid_2, sid_large,
fapl=H5P_DEFAULT, dcpl=H5P_DEFAULT, gid1, gid2, cmp_tid, tid_str,
tid_enum, tid_array_f, tid_vlen_i, tid_vlen_s;
char name[32], tmp_name1[32], tmp_name2[32], tmp_name3[32];
hsize_t dims[1]={dim0}, dims2d[2]={dim0, (dim0/4+1)}, dims_array[1]={FIXED_LEN},
dim1[1]={2};
char *enum_names[4] = {"SOLID", "LIQUID", "GAS", "PLASMA"};
test_comp_t *buf_comp=NULL, *buf_comp_large=NULL;
int *buf_int=NULL;
float (*buf_float_a)[FIXED_LEN]=NULL;
double **buf_double2d=NULL;
hvl_t *buf_vlen_i=NULL;
char (*buf_str)[FIXED_LEN];
char **buf_vlen_s=NULL;
hobj_ref_t buf_ref[2];
hdset_reg_ref_t buf_reg_ref[2];
size_t offset, len;
herr_t status;
char *names[NTYPES] = { "int", "ulong", "float", "double", "fixed string",
"enum", "fixed float array", "vlen int array", "vlen strings"};
hid_t types[NTYPES] = { H5T_NATIVE_INT, H5T_NATIVE_UINT64, H5T_NATIVE_FLOAT,
H5T_NATIVE_DOUBLE, tid_str, tid_enum, tid_array_f, tid_vlen_i, tid_vlen_s};
hsize_t coords[4][2] = { {0, 1}, {3, 5}, {1, 0}, {2, 4}}, start=0, stride=1, count=1;
if (nrows < NROWS) nrows = NROWS;
if (ngrps<NGROUPS) ngrps=NGROUPS;
if (ndsets<NDSETS) ndsets=NDSETS;
if (nattrs<NATTRS) nattrs=NATTRS;
if (dim0<DIM0) dim0=DIM0;
if (chunk>dim0) chunk=dim0/4;
if (chunk<1) chunk = 1;
if (vlen<1) vlen = MAXVLEN;
/* create fixed string datatype */
types[4] = tid_str = H5Tcopy (H5T_C_S1);
H5Tset_size (tid_str, FIXED_LEN);
/* create enum datatype */
types[5] = tid_enum = H5Tenum_create(H5T_NATIVE_INT);
for (i = (int) SOLID; i <= (int) PLASMA; i++) {
phase_t val = (phase_t) i;
status = H5Tenum_insert (tid_enum, enum_names[i], &val);
}
/* create float array datatype */
types[6] = tid_array_f = H5Tarray_create (H5T_NATIVE_FLOAT, 1, dims_array);
/* create variable length integer datatypes */
types[7] = tid_vlen_i = H5Tvlen_create (H5T_NATIVE_INT);
/* create variable length string datatype */
types[8] = tid_vlen_s = H5Tcopy (H5T_C_S1);
H5Tset_size (tid_vlen_s, H5T_VARIABLE);
/* create compound datatypes */
cmp_tid = H5Tcreate (H5T_COMPOUND, sizeof (test_comp_t));
offset = 0;
for (i=0; i<NTYPES-2; i++) {
H5Tinsert(cmp_tid, names[i], offset, types[i]);
offset += H5Tget_size(types[i]);
}
H5Tinsert(cmp_tid, names[7], offset, types[7]);
offset += sizeof (hvl_t);
H5Tinsert(cmp_tid, names[8], offset, types[8]);
/* create dataspace */
sid_1d = H5Screate_simple (1, dims, NULL);
sid_2d = H5Screate_simple (2, dims2d, NULL);
sid_2 = H5Screate_simple (1, dim1, NULL);
sid_large = H5Screate_simple (1, &nrows, NULL);
sid_null = H5Screate (H5S_NULL);
sid_scalar = H5Screate (H5S_SCALAR);
/* create fid access property */
fapl = H5Pcreate (H5P_FILE_ACCESS);
H5Pset_libver_bounds (fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST);
/* create dataset creation property */
dcpl = H5Pcreate (H5P_DATASET_CREATE);
/* set dataset chunk */
if (chunk>0) {
H5Pset_chunk (dcpl, 1, &chunk);
}
/* set dataset compression */
if (compressed) {
if (chunk<=0) {
chunk = dim0/10+1;;
H5Pset_chunk (dcpl, 1, &chunk);
}
H5Pset_shuffle (dcpl);
H5Pset_deflate (dcpl, 6);
}
/* allocate buffers */
buf_comp = (test_comp_t *)calloc(dim0, sizeof(test_comp_t));
buf_comp_large = (test_comp_t *)calloc(nrows, sizeof(test_comp_t));
buf_int = (int *)calloc(dim0, sizeof(int));
buf_float_a = malloc(dim0*sizeof(*buf_float_a));
buf_vlen_i = (hvl_t *)calloc(dim0, sizeof (hvl_t));
buf_vlen_s = (char **)calloc(dim0, sizeof(char *));
buf_str = malloc(dim0*sizeof (*buf_str));
/* allocate array of doulbe pointers */
buf_double2d = (double **)calloc(dims2d[0],sizeof(double *));
/* allocate a contigous chunk of memory for the data */
buf_double2d[0] = (double *)calloc( dims2d[0]*dims2d[1],sizeof(double) );
/* assign memory city to pointer array */
for (i=1; i <dims2d[0]; i++) buf_double2d[i] = buf_double2d[0]+i*dims2d[1];
/* fill buffer values */
len = 1;
for (i=0; i<dims[0]; i++) {
buf_comp[i].i = buf_int[i] = i-2147483648;
buf_comp[i].l = 0xffffffffffffffff-i;
buf_comp[i].f = 1.0/(i+1.0);
buf_comp[i].d = 987654321.0*i+1.0/(i+1.0);
buf_comp[i].e = (phase_t) (i % (int) (PLASMA + 1));
for (j=0; j<FIXED_LEN; j++) {
buf_comp[i].f_array[j] = buf_float_a[i][j] = i*100+j;
buf_str[i][j] = 'a' + (i%26);
}
buf_str[i][FIXED_LEN-1] = 0;
strcpy(buf_comp[i].s, buf_str[i]);
len = (1-cos(i/8.0))/2*vlen+1;
if (!i) len = vlen;
buf_vlen_i[i].len = len;
buf_vlen_i[i].p = (int *)calloc(len, sizeof(int));
for (j=0; j<len; j++) ((int*)(buf_vlen_i[i].p))[j] = i*100+j;
buf_comp[i].i_vlen = buf_vlen_i[i];
buf_vlen_s[i] = (char *)calloc(len, sizeof(char));
for (j=0; j<len-1; j++)
buf_vlen_s[i][j] = j%26+'A';
buf_comp[i].s_vlen = buf_vlen_s[i];
for (j=0; j<dims2d[1]; j++)
buf_double2d[i][j] = i+j/10000.0;
}
for (i=0; i<nrows; i++) {
buf_comp_large[i].i = i-2147483648;
buf_comp_large[i].l = 0xffffffffffffffff-i;
buf_comp_large[i].f = 1.0/(i+1.0);
buf_comp_large[i].d = 987654321.0*i+1.0/(i+1.0);
buf_comp_large[i].e = (phase_t) (i % (int) (PLASMA + 1));
for (j=0; j<FIXED_LEN-1; j++) {
buf_comp_large[i].f_array[j] = i*100+j;
buf_comp_large[i].s[j] = 'a' + (i%26);
}
len = i%vlen+1;
buf_comp_large[i].i_vlen.len = len;
buf_comp_large[i].i_vlen.p = (int *)calloc(len, sizeof(int));
for (j=0; j<len; j++) ((int*)(buf_comp_large[i].i_vlen.p))[j] = i*100+j;
buf_comp_large[i].s_vlen = (char *)calloc(i+2, sizeof(char));
for (j=0; j<i+1; j++) (buf_comp_large[i].s_vlen)[j] = j%26+'A';
}
/* create file */
if (latest)
fid = H5Fcreate (fname, H5F_ACC_TRUNC, H5P_DEFAULT, fapl);
else
fid = H5Fcreate (fname, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
add_attrs(fid, 0);
sprintf(name, "a cmp ds of %d rows", nrows);
did = H5Dcreate (fid, name, cmp_tid, sid_large, H5P_DEFAULT, dcpl, H5P_DEFAULT);
H5Dwrite (did, cmp_tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf_comp_large);
add_attrs(did, 0);
H5Dclose(did);
// /* add attributes*/
gid1 = H5Gcreate (fid, "attributes", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (nattrs<1) nattrs = 1;
i=0;
while (i<nattrs) i += add_attrs(gid1, i);
H5Gclose(gid1);
/* add many sub groups to a group*/
gid1 = H5Gcreate (fid, "groups", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
add_attrs(gid1, 0);
for (i=0; i<ngrps; i++) {
/* create sub groups */
sprintf(name, "g%02d", i);
gid2 = H5Gcreate (gid1, name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (i<10) add_attrs(gid2, 0);
H5Gclose(gid2);
}
H5Gclose(gid1);
/* add many datasets to a group */
gid1 = H5Gcreate (fid, "datasets", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
add_attrs(gid1, 0);
for (j=0; j<ndsets; j+=12) {
/* 1 add a null dataset */
sprintf(name, "%05d null dataset", j);
did = H5Dcreate (gid1, name, H5T_STD_I32LE, sid_null, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (!j) add_attrs(did, j);
H5Dclose(did);
/* 2 add scalar int point */
sprintf(name, "%05d scalar int point", j);
did = H5Dcreate (gid1, name, H5T_NATIVE_INT, sid_scalar, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Dwrite (did, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, &j);
if (!j) add_attrs(did, j);
H5Dclose(did);
/* 3 scalar vlen string */
sprintf(name, "%05d scalar vlen string", j);
did = H5Dcreate (gid1, name, tid_vlen_s, sid_scalar, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Dwrite (did, tid_vlen_s, H5S_ALL, H5S_ALL, H5P_DEFAULT, &buf_vlen_s[0]);
if (!j) add_attrs(did, j);
H5Dclose(did);
/* 4 add fixed-length float array */
sprintf(name, "%05d fixed-length float array", j);
did = H5Dcreate (gid1, name, tid_array_f, sid_1d, H5P_DEFAULT, dcpl, H5P_DEFAULT);
H5Dwrite (did, tid_array_f, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf_float_a);
if (!j) add_attrs(did, j);
H5Dclose(did);
/* 5 add fixed-length strings */
sprintf(name, "%05d fixed-length strings", j);
did = H5Dcreate (gid1, name, tid_str, sid_1d, H5P_DEFAULT, dcpl, H5P_DEFAULT);
H5Dwrite (did, tid_str, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf_str);
if (!j) add_attrs(did, j);
H5Dclose(did);
/* 6 add compound data */
sprintf(name, "%05d compund data", j);
did = H5Dcreate (gid1, name, cmp_tid, sid_1d, H5P_DEFAULT, dcpl, H5P_DEFAULT);
H5Dwrite (did, cmp_tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf_comp);
if (!j) add_attrs(did, j);
H5Dclose(did);
/* 7 add 2D double */
sprintf(name, "%05d 2D double", j);
strcpy (tmp_name1, name);
did = H5Dcreate (gid1, name, H5T_NATIVE_DOUBLE, sid_2d, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Dwrite (did, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf_double2d[0]);
if (!j) add_attrs(did, j);
H5Dclose(did);
/* 8 add 1D int array */
sprintf(name, "%05d 1D int array", j);
did = H5Dcreate (gid1, name, H5T_NATIVE_INT, sid_1d, H5P_DEFAULT, dcpl, H5P_DEFAULT);
H5Dwrite (did, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf_int);
if (!j) add_attrs(did, j);
H5Dclose(did);
/* 9 add vlen int array */
sprintf(name, "%05d vlen int array", j);
strcpy (tmp_name2, name);
did = H5Dcreate (gid1, name, tid_vlen_i, sid_1d, H5P_DEFAULT, dcpl, H5P_DEFAULT);
H5Dwrite (did, tid_vlen_i, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf_vlen_i);
if (!j) add_attrs(did, j);
H5Dclose(did);
/* 10 add vlen strings */
sprintf(name, "%05d vlen strings", j);
strcpy (tmp_name3, name);
did = H5Dcreate (gid1, name, tid_vlen_s, sid_1d, H5P_DEFAULT, dcpl, H5P_DEFAULT);
H5Dwrite (did, tid_vlen_s, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf_vlen_s);
if (!j) add_attrs(did, j);
H5Dclose(did);
/* 11 add object refs */
H5Rcreate(&buf_ref[0],gid1, ".", H5R_OBJECT, -1);
H5Rcreate(&buf_ref[1],gid1, tmp_name3, H5R_OBJECT, -1);
sprintf(name, "%05d obj refs", j);
did = H5Dcreate (gid1, name, H5T_STD_REF_OBJ, sid_2, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Dwrite (did, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf_ref);
if (!j) add_attrs(did, j);
H5Dclose(did);
/* 12 add region refs */
H5Sselect_elements (sid_2d, H5S_SELECT_SET, 4, coords[0]);
H5Rcreate(&buf_reg_ref[0],gid1, tmp_name1, H5R_DATASET_REGION, sid_2d);
H5Sselect_none(sid_2d);
count = dims[0]/2+1;
H5Sselect_hyperslab (sid_1d, H5S_SELECT_SET, &start, &stride, &count,NULL);
H5Rcreate(&buf_reg_ref[1],gid1, tmp_name2, H5R_DATASET_REGION, sid_1d);
H5Sselect_none(sid_1d);
sprintf(name, "%05d region refs", j);
did = H5Dcreate (gid1, name, H5T_STD_REF_DSETREG, sid_2, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Dwrite (did, H5T_STD_REF_DSETREG, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf_reg_ref);
if (!j) add_attrs(did, j);
H5Dclose(did);
}
H5Gclose(gid1);
H5Tclose (tid_array_f);
H5Tclose (tid_vlen_i);
H5Tclose (tid_vlen_s);
H5Tclose (tid_enum);
H5Tclose (tid_str);
H5Tclose (cmp_tid);
H5Pclose (dcpl);
H5Pclose (fapl);
H5Sclose (sid_1d);
H5Sclose (sid_2d);
H5Sclose (sid_2);
H5Sclose (sid_large);
H5Sclose (sid_null);
H5Sclose (sid_scalar);
H5Fclose (fid);
for (i=0; i<dims[0]; i++) {
if (buf_vlen_i[i].p) free(buf_vlen_i[i].p);
if (buf_vlen_s[i]) free(buf_vlen_s[i]);
}
for (i=0; i<nrows; i++) {
if (buf_comp_large[i].i_vlen.p) free(buf_comp_large[i].i_vlen.p);
if (buf_comp_large[i].s_vlen) free(buf_comp_large[i].s_vlen);
}
free (buf_comp);
free (buf_comp_large);
free (buf_int);
free (buf_float_a);
free (buf_double2d[0]);
free (buf_double2d);
free (buf_str);
free(buf_vlen_i);
free(buf_vlen_s);
return 0;
}
/*
adds different types of attributes to an object.
returns the number of attributes added to the objects.
*/
int add_attrs(hid_t oid, int idx)
{
char name[32];
int i0, i1, i2, j, nattrs=0;
hid_t aid, tid, tid1, sid;
hvl_t i_vlen[4];
hobj_ref_t ref;
zipcode_t cmp_data[4];
unsigned int i = 0xffffffff;
long long l = -2147483647;
float f = 123456789.987654321;
double d = 987654321.123456789;
char *s[7] = {"Parting", "is such", "sweeter", "sorrow."};
float f_array[4] = {1.0, 2.22, 3.333, 4.444};
char *s_vlen[4] = {"Parting", "is such", "sweet", "sorrow."};
hsize_t dims1[1]={1}, dims2[1]={4}, dims3[2]={3,5};
int int3d[4][3][5];
size_t offset = 0;
for (i0=0; i0<4; i0++) {
i_vlen[i0].len = (i0+1);
i_vlen[i0].p = (int *)calloc(i_vlen[i0].len, sizeof(int));
for (j=0; j<i_vlen[i0].len; j++)
((int *)i_vlen[i0].p)[j] = i0*100+j;
for (i1=0; i1<3; i1++) {
for (i2=0; i2<5; i2++)
int3d[i0][i1][i2] = i0*i1-i1*i2+i0*i2;
}
}
cmp_data[0].zipcode = 01001;
cmp_data[0].city = "Agawam, Massachusetts";
cmp_data[1].zipcode = 99950;
cmp_data[1].city = "Ketchikan, Alaska";
cmp_data[2].zipcode = 00501;
cmp_data[2].city = "Holtsville, New York";
cmp_data[3].zipcode = 61820;
cmp_data[3].city = "Champaign, Illinois";
/* 1 scalar point */
sid = H5Screate (H5S_SCALAR);
sprintf(name, "%05d scalar int", idx);
nattrs += add_attr(oid, name, H5T_NATIVE_UINT, sid, &i);
sprintf(name, "%05d scalar ulong", idx);
nattrs += add_attr(oid, name, H5T_NATIVE_INT64, sid, &l);
sprintf(name, "%05d scalar str", idx);
tid = H5Tcopy (H5T_C_S1);
H5Tset_size (tid, H5T_VARIABLE);
nattrs += add_attr(oid, name, tid, sid, &s[2]);
H5Tclose(tid);
H5Sclose(sid);
/* 4 single point */
sid = H5Screate_simple (1, dims1, NULL);
H5Rcreate(&ref, oid, ".", H5R_OBJECT, -1);
sprintf(name, "%05d single float", idx);
nattrs += add_attr(oid, name, H5T_NATIVE_FLOAT, sid, &f);
sprintf(name, "%05d single double", idx);
nattrs += add_attr(oid, name, H5T_NATIVE_DOUBLE, sid, &d);
sprintf(name, "%05d single obj_ref", idx);
nattrs += add_attr(oid, name, H5T_STD_REF_OBJ, sid, &ref);
H5Sclose(sid);
/* 7 fixed length 1D array */
sid = H5Screate_simple (1, dims1, NULL);
tid = H5Tarray_create (H5T_NATIVE_FLOAT, 1, dims2);
sprintf(name, "%05d array float", idx);
nattrs += add_attr(oid, name, tid, sid, &f_array[0]);
H5Tclose(tid);
tid = H5Tcopy (H5T_C_S1);
H5Tset_size (tid, strlen(s[0])+1);
tid1 = H5Tarray_create (tid, 1, dims2);
sprintf(name, "%05d array str", idx);
nattrs += add_attr(oid, name, tid1, sid, s);
H5Tclose(tid1);
H5Tclose(tid);
H5Sclose(sid);
/* 9 fixed length 2D int arrays */
sid = H5Screate_simple (1, dims2, NULL);
tid = H5Tarray_create (H5T_NATIVE_INT, 2, dims3);
sprintf(name, "%05d array int 2D", idx);
nattrs += add_attr(oid, name, tid, sid, int3d[0][0]);
H5Tclose(tid);
H5Sclose(sid);
/* 10 variable length arrays */
sid = H5Screate_simple (1, dims2, NULL);
tid = H5Tcopy (H5T_C_S1);
H5Tset_size (tid, H5T_VARIABLE);
sprintf(name, "%05d vlen strings", idx);
nattrs += add_attr(oid, name, tid, sid, s_vlen);
H5Tclose(tid);
tid = H5Tvlen_create (H5T_NATIVE_INT);;
sprintf(name, "%05d vlen int array", idx);
nattrs += add_attr(oid, name, tid, sid, i_vlen);
H5Tclose(tid);
H5Sclose(sid);
/* 12 compound data */
sid = H5Screate_simple (1, dims2, NULL);
tid = H5Tcreate (H5T_COMPOUND, sizeof (zipcode_t));
tid1 = H5Tcopy (H5T_C_S1);
H5Tset_size (tid1, H5T_VARIABLE);
H5Tinsert (tid, "zip code", 0, H5T_NATIVE_INT); offset += sizeof(H5T_NATIVE_INT);
H5Tinsert (tid, "City", offset, tid1); offset += sizeof(char *);
sprintf(name, "%05d compound data", idx);
nattrs += add_attr(oid, name, tid, sid, cmp_data);
H5Tclose(tid1);
H5Tclose(tid);
H5Sclose(sid);
for (i0=0; i0<4; i0++)
free(i_vlen[i0].p);
return nattrs;
}
herr_t H5IMlink_palette( hid_t loc_id,
const char *image_name,
const char *pal_name )
{
hid_t did;
hid_t atid=-1;
hid_t aid=-1;
hid_t asid=-1;
hobj_ref_t ref; /* write a new reference */
hobj_ref_t *refbuf; /* buffer to read references */
hssize_t n_refs;
hsize_t dim_ref;
int ok_pal;
/* check the arguments */
if (image_name == NULL)
return -1;
if (pal_name == NULL)
return -1;
/* The image dataset may or may not have the attribute "PALETTE"
* First we try to open to see if it is already there; if not, it is created.
* If it exists, the array of references is extended to hold the reference
* to the new palette
*/
/* First we get the image id */
if((did = H5Dopen2(loc_id, image_name, H5P_DEFAULT)) < 0)
return -1;
/* Try to find the attribute "PALETTE" on the >>image<< dataset */
ok_pal = H5LT_find_attribute( did, "PALETTE" );
/*-------------------------------------------------------------------------
* It does not exist. We create the attribute and one reference
*-------------------------------------------------------------------------
*/
if(ok_pal == 0 )
{
if((asid = H5Screate(H5S_SCALAR)) < 0)
goto out;
/* Create the attribute type for the reference */
if((atid = H5Tcopy(H5T_STD_REF_OBJ)) < 0)
goto out;
/* Create the attribute "PALETTE" to be attached to the image*/
if((aid = H5Acreate2(did, "PALETTE", atid, asid, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto out;
/* Create a reference. The reference is created on the local id. */
if(H5Rcreate(&ref, loc_id, pal_name, H5R_OBJECT, (hid_t)-1) < 0)
goto out;
/* Write the attribute with the reference */
if(H5Awrite(aid, atid, &ref) < 0)
goto out;
/* close */
if(H5Sclose(asid) < 0)
goto out;
if(H5Tclose(atid) < 0)
goto out;
if(H5Aclose(aid) < 0)
goto out;
}
/*-------------------------------------------------------------------------
* The attribute already exists, open it
*-------------------------------------------------------------------------
*/
else if(ok_pal == 1)
{
if((aid = H5Aopen(did, "PALETTE", H5P_DEFAULT)) < 0)
goto out;
if((atid = H5Aget_type(aid)) < 0)
goto out;
if(H5Tget_class(atid) < 0)
goto out;
/* Get and save the old reference(s) */
if((asid = H5Aget_space(aid)) < 0)
goto out;
n_refs = H5Sget_simple_extent_npoints(asid);
dim_ref = (hsize_t)n_refs + 1;
refbuf = (hobj_ref_t*)HDmalloc( sizeof(hobj_ref_t) * (size_t)dim_ref );
if ( H5Aread( aid, atid, refbuf ) < 0)
goto out;
/* The attribute must be deleted, in order to the new one can reflect the changes*/
if(H5Adelete(did, "PALETTE") < 0)
goto out;
/* Create a new reference for this palette. */
if ( H5Rcreate( &ref, loc_id, pal_name, H5R_OBJECT, (hid_t)-1 ) < 0)
goto out;
refbuf[n_refs] = ref;
/* Create the data space for the new references */
if(H5Sclose(asid) < 0)
goto out;
if((asid = H5Screate_simple(1, &dim_ref, NULL)) < 0)
goto out;
/* Create the attribute again with the changes of space */
if(H5Aclose(aid) < 0)
goto out;
if((aid = H5Acreate2(did, "PALETTE", atid, asid, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto out;
/* Write the attribute with the new references */
if(H5Awrite(aid, atid, refbuf) < 0)
goto out;
/* close */
if(H5Sclose(asid) < 0)
goto out;
if(H5Tclose(atid) < 0)
goto out;
if(H5Aclose(aid) < 0)
goto out;
HDfree( refbuf );
} /* ok_pal == 1 */
/* Close the image dataset. */
if ( H5Dclose( did ) < 0)
return -1;
return 0;
out:
H5Dclose( did );
H5Sclose( asid );
H5Tclose( atid );
H5Aclose( aid );
return -1;
}
int
main (void)
{
hid_t file, space, dset, obj, attr; /* Handles */
herr_t status;
hsize_t dims[1] = {DIM0};
hobj_ref_t wdata[DIM0], /* Write buffer */
*rdata; /* Read buffer */
H5G_obj_t objtype;
ssize_t size;
char *name;
int ndims,
i;
/*
* Create a new file using the default properties.
*/
file = H5Fcreate (FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create a dataset with a scalar dataspace.
*/
space = H5Screate (H5S_SCALAR);
obj = H5Dcreate (file, "DS2", H5T_STD_I32LE, space, H5P_DEFAULT);
status = H5Dclose (obj);
status = H5Sclose (space);
/*
* Create a group.
*/
obj = H5Gcreate (file, "G1", H5P_DEFAULT);
status = H5Gclose (obj);
/*
* Create references to the previously created objects. Passing -1
* as space_id causes this parameter to be ignored. Other values
* besides valid dataspaces result in an error.
*/
status = H5Rcreate (&wdata[0], file, "G1", H5R_OBJECT, -1);
status = H5Rcreate (&wdata[1], file, "DS2", H5R_OBJECT, -1);
/*
* Create dataset with a scalar dataspace to serve as the parent
* for the attribute.
*/
space = H5Screate (H5S_SCALAR);
dset = H5Dcreate (file, DATASET, H5T_STD_I32LE, space, H5P_DEFAULT);
status = H5Sclose (space);
/*
* Create dataspace. Setting maximum size to NULL sets the maximum
* size to be the current size.
*/
space = H5Screate_simple (1, dims, NULL);
/*
* Create the attribute and write the object references to it.
*/
attr = H5Acreate (dset, ATTRIBUTE, H5T_STD_REF_OBJ, space, H5P_DEFAULT);
status = H5Awrite (attr, H5T_STD_REF_OBJ, wdata);
/*
* Close and release resources.
*/
status = H5Aclose (attr);
status = H5Dclose (dset);
status = H5Sclose (space);
status = H5Fclose (file);
/*
* Now we begin the read section of this example. Here we assume
* the attribute has the same name and rank, but can have any size.
* Therefore we must allocate a new array to read in data using
* malloc().
*/
/*
* Open file, dataset, and attribute.
*/
file = H5Fopen (FILE, H5F_ACC_RDONLY, H5P_DEFAULT);
dset = H5Dopen (file, DATASET);
attr = H5Aopen_name (dset, ATTRIBUTE);
/*
* Get dataspace and allocate memory for read buffer.
*/
space = H5Aget_space (attr);
ndims = H5Sget_simple_extent_dims (space, dims, NULL);
rdata = (hobj_ref_t *) malloc (dims[0] * sizeof (hobj_ref_t));
/*
* Read the data.
*/
status = H5Aread (attr, H5T_STD_REF_OBJ, rdata);
/*
* Output the data to the screen.
*/
for (i=0; i<dims[0]; i++) {
printf ("%s[%d]:\n ->", ATTRIBUTE, i);
/*
* Open the referenced object, get its name and type.
*/
obj = H5Rdereference (dset, H5R_OBJECT, &rdata[i]);
objtype = H5Rget_obj_type (dset, H5R_OBJECT, &rdata[i]);
/*
* Get the length of the name, allocate space, then retrieve
* the name.
*/
size = 1 + H5Iget_name (obj, NULL, 0);
if (size > 1) {
name = (char *) malloc (size);
size = 1 + H5Iget_name (obj, name, size);
}
/*
* Print the object type and close the object.
*/
switch (objtype) {
case H5G_GROUP:
printf ("Group");
status = H5Gclose (obj);
break;
case H5G_DATASET:
printf ("Dataset");
status = H5Dclose (obj);
break;
case H5G_TYPE:
printf ("Named Datatype");
status = H5Tclose (obj);
}
/*
* Print the name and deallocate space for the name.
*/
if (size > 1) {
printf (": %s", name);
free (name);
}
printf ("\n");
}
/*
* Close and release resources.
*/
free (rdata);
status = H5Aclose (attr);
status = H5Dclose (dset);
status = H5Sclose (space);
status = H5Fclose (file);
return 0;
}
/*-------------------------------------------------------------------------
* Function: gen_region_ref
*
* Purpose: Generate dataset region references
*
* Programmer: Jonathan Kim (Feb 23, 2010)
*------------------------------------------------------------------------*/
static herr_t gen_region_ref(hid_t loc_id)
{
hid_t sid=0, oid1=0, oid2=0;
int status;
herr_t ret = SUCCEED;
char data[3][16] = {"The quick brown", "fox jumps over ", "the 5 lazy dogs"};
hsize_t dims2[2] = {3,16};
hsize_t coords[4][2] = { {0,1}, {2,11}, {1,0}, {2,4} };
hdset_reg_ref_t rr_data[2];
hsize_t start[2] = {0,0};
hsize_t stride[2] = {2,11};
hsize_t count[2] = {2,2};
hsize_t block[2] = {1,3};
hsize_t dims1[1] = {2};
sid = H5Screate_simple (2, dims2, NULL);
if (sid < 0)
{
fprintf(stderr, "Error: %s %d> H5Screate_simple failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
/* create normal dataset which is refered */
oid2 = H5Dcreate2 (loc_id, REG_REF_DS2, H5T_STD_I8LE, sid, H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
if (oid2 < 0)
{
fprintf(stderr, "Error: %s %d> H5Dcreate2 failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
/* write values to dataset */
status = H5Dwrite (oid2, H5T_NATIVE_CHAR, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> H5Dwrite failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
/* select elements space for reference */
status = H5Sselect_elements (sid, H5S_SELECT_SET, 4, coords[0]);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> H5Sselect_elements failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
/* create region reference from elements space */
status = H5Rcreate (&rr_data[0], loc_id, REG_REF_DS2, H5R_DATASET_REGION, sid);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
/* select hyperslab space for reference */
status = H5Sselect_hyperslab (sid, H5S_SELECT_SET, start, stride, count, block);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> H5Sselect_hyperslab failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
/* create region reference from hyperslab space */
status = H5Rcreate (&rr_data[1], loc_id, REG_REF_DS2, H5R_DATASET_REGION, sid);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
H5Sclose (sid);
/* Create dataspace. */
sid = H5Screate_simple (1, dims1, NULL);
if (sid < 0)
{
fprintf(stderr, "Error: %s %d> H5Screate_simple failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
/* create region reference dataset */
oid1 = H5Dcreate2 (loc_id, REG_REF_DS1, H5T_STD_REF_DSETREG, sid, H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
if (oid1 < 0)
{
fprintf(stderr, "Error: %s %d> H5Dcreate2 failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
/* write data as region references */
status = H5Dwrite (oid1, H5T_STD_REF_DSETREG, H5S_ALL, H5S_ALL, H5P_DEFAULT, rr_data);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> H5Dwrite failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
out:
if (oid1 > 0)
H5Dclose (oid1);
if (oid2 > 0)
H5Dclose (oid2);
if (sid > 0)
H5Sclose (sid);
return ret;
}
/*-------------------------------------------------------------------------
* Function: gen_obj_ref
*
* Purpose: Generate object references to dataset and group
*
* Programmer: Jonathan Kim (Feb 23, 2010)
*------------------------------------------------------------------------*/
static herr_t gen_obj_ref(hid_t loc_id)
{
hid_t sid=0, oid=0;
hsize_t dims1[1]={3};
hsize_t dims2[1]={2};
int data[3] = {10,20,30};
int status;
/*---------------------
* create obj references to the previously created objects.
* Passing -1 as reference is an object.*/
hobj_ref_t or_data[2]; /* write buffer */
herr_t ret = SUCCEED;
/*--------------
* add dataset */
sid = H5Screate_simple(1, dims1, NULL);
if (sid < 0)
{
fprintf(stderr, "Error: %s %d> H5Screate_simple failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
oid = H5Dcreate2 (loc_id, OBJ_REF_DS, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (oid < 0)
{
fprintf(stderr, "Error: %s %d> H5Dcreate2 failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
status = H5Dwrite(oid, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> H5Dwrite failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
H5Dclose(oid);
H5Sclose(sid);
/*--------------
* add group */
oid = H5Gcreate2 (loc_id, OBJ_REF_GRP, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (oid < 0)
{
fprintf(stderr, "Error: %s %d> H5Gcreate2 failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
H5Gclose(oid);
status = H5Rcreate (&or_data[0], loc_id, OBJ_REF_DS, H5R_OBJECT, -1);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
status = H5Rcreate (&or_data[1], loc_id, OBJ_REF_GRP, H5R_OBJECT, -1);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> H5Rcreate failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
sid = H5Screate_simple (1, dims2, NULL);
if (sid < 0)
{
fprintf(stderr, "Error: %s %d> H5Screate_simple failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
oid = H5Dcreate2 (loc_id, "Dset_OBJREF", H5T_STD_REF_OBJ, sid, H5P_DEFAULT,H5P_DEFAULT,H5P_DEFAULT);
if (oid < 0)
{
fprintf(stderr, "Error: %s %d> H5Dcreate2 failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
status = H5Dwrite(oid, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, or_data);
if (status < 0)
{
fprintf(stderr, "Error: %s %d> H5Dwrite failed.\n", FUNC, __LINE__);
ret = FAIL;
goto out;
}
out:
if(oid > 0)
H5Dclose(oid);
if(sid > 0)
H5Sclose(sid);
return ret;
}
int
main(void) {
hid_t fid1; /* HDF5 File IDs */
hid_t dataset; /* Dataset ID */
hid_t group; /* Group ID */
hid_t sid1; /* Dataspace ID */
hid_t tid1; /* Datatype ID */
hsize_t dims1[] = {SPACE1_DIM1};
hobj_ref_t *wbuf; /* buffer to write to disk */
int *tu32; /* Temporary pointer to int data */
int i; /* counting variables */
const char *write_comment="Foo!"; /* Comments for group */
herr_t ret; /* Generic return value */
/* Compound datatype */
typedef struct s1_t {
unsigned int a;
unsigned int b;
float c;
} s1_t;
/* Allocate write buffers */
wbuf=(hobj_ref_t *)malloc(sizeof(hobj_ref_t)*SPACE1_DIM1);
tu32=malloc(sizeof(int)*SPACE1_DIM1);
/* Create file */
fid1 = H5Fcreate(FILE1, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/* Create dataspace for datasets */
sid1 = H5Screate_simple(SPACE1_RANK, dims1, NULL);
/* Create a group */
group=H5Gcreate(fid1,"Group1",-1);
/* Set group's comment */
ret=H5Gset_comment(group,".",write_comment);
/* Create a dataset (inside Group1) */
dataset=H5Dcreate(group,"Dataset1",H5T_STD_U32LE,sid1,H5P_DEFAULT);
for(i=0; i<SPACE1_DIM1; i++)
tu32[i] = i*3;
/* Write selection to disk */
ret=H5Dwrite(dataset,H5T_NATIVE_INT,H5S_ALL,H5S_ALL,H5P_DEFAULT,tu32);
/* Close Dataset */
ret = H5Dclose(dataset);
/* Create another dataset (inside Group1) */
dataset=H5Dcreate(group,"Dataset2",H5T_NATIVE_UCHAR,sid1,H5P_DEFAULT);
/* Close Dataset */
ret = H5Dclose(dataset);
/* Create a datatype to refer to */
tid1 = H5Tcreate (H5T_COMPOUND, sizeof(s1_t));
/* Insert fields */
ret=H5Tinsert (tid1, "a", HOFFSET(s1_t,a), H5T_NATIVE_INT);
ret=H5Tinsert (tid1, "b", HOFFSET(s1_t,b), H5T_NATIVE_INT);
ret=H5Tinsert (tid1, "c", HOFFSET(s1_t,c), H5T_NATIVE_FLOAT);
/* Save datatype for later */
ret=H5Tcommit (group, "Datatype1", tid1);
/* Close datatype */
ret = H5Tclose(tid1);
/* Close group */
ret = H5Gclose(group);
/* Create a dataset to store references */
dataset=H5Dcreate(fid1,"Dataset3",H5T_STD_REF_OBJ,sid1,H5P_DEFAULT);
/* Create reference to dataset */
ret = H5Rcreate(&wbuf[0],fid1,"/Group1/Dataset1",H5R_OBJECT,-1);
/* Create reference to dataset */
ret = H5Rcreate(&wbuf[1],fid1,"/Group1/Dataset2",H5R_OBJECT,-1);
/* Create reference to group */
ret = H5Rcreate(&wbuf[2],fid1,"/Group1",H5R_OBJECT,-1);
/* Create reference to named datatype */
ret = H5Rcreate(&wbuf[3],fid1,"/Group1/Datatype1",H5R_OBJECT,-1);
/* Write selection to disk */
ret=H5Dwrite(dataset,H5T_STD_REF_OBJ,H5S_ALL,H5S_ALL,H5P_DEFAULT,wbuf);
/* Close disk dataspace */
ret = H5Sclose(sid1);
/* Close Dataset */
ret = H5Dclose(dataset);
/* Close file */
ret = H5Fclose(fid1);
free(wbuf);
free(tu32);
return 0;
}
int
main (void)
{
hid_t file, space, memspace, dset, dset2, attr;
/* Handles */
herr_t status;
hsize_t dims[1] = {DIM0},
dims2[2] = {DS2DIM0, DS2DIM1},
coords[4][2] = { {0, 1},
{2, 11},
{1, 0},
{2, 4} },
start[2] = {0, 0},
stride[2] = {2, 11},
count[2] = {2, 2},
block[2] = {1, 3};
hssize_t npoints;
hdset_reg_ref_t wdata[DIM0], /* Write buffer */
*rdata; /* Read buffer */
ssize_t size;
char wdata2[DS2DIM0][DS2DIM1] = {"The quick brown",
"fox jumps over ",
"the 5 lazy dogs"},
*rdata2,
*name;
int ndims,
i;
/*
* Create a new file using the default properties.
*/
file = H5Fcreate (FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create a dataset with character data.
*/
space = H5Screate_simple (2, dims2, NULL);
dset2 = H5Dcreate (file, DATASET2, H5T_STD_I8LE, space, H5P_DEFAULT,
H5P_DEFAULT, H5P_DEFAULT);
status = H5Dwrite (dset2, H5T_NATIVE_CHAR, H5S_ALL, H5S_ALL, H5P_DEFAULT,
wdata2);
/*
* Create reference to a list of elements in dset2.
*/
status = H5Sselect_elements (space, H5S_SELECT_SET, 4, coords[0]);
status = H5Rcreate (&wdata[0], file, DATASET2, H5R_DATASET_REGION, space);
/*
* Create reference to a hyperslab in dset2, close dataspace.
*/
status = H5Sselect_hyperslab (space, H5S_SELECT_SET, start, stride, count,
block);
status = H5Rcreate (&wdata[1], file, DATASET2, H5R_DATASET_REGION, space);
status = H5Sclose (space);
/*
* Create dataset with a null dataspace to serve as the parent for
* the attribute.
*/
space = H5Screate (H5S_NULL);
dset = H5Dcreate (file, DATASET, H5T_STD_I32LE, space, H5P_DEFAULT,
H5P_DEFAULT, H5P_DEFAULT);
status = H5Sclose (space);
/*
* Create dataspace. Setting maximum size to NULL sets the maximum
* size to be the current size.
*/
space = H5Screate_simple (1, dims, NULL);
/*
* Create the attribute and write the region references to it.
*/
attr = H5Acreate (dset, ATTRIBUTE, H5T_STD_REF_DSETREG, space, H5P_DEFAULT,
H5P_DEFAULT);
status = H5Awrite (attr, H5T_STD_REF_DSETREG, wdata);
/*
* Close and release resources.
*/
status = H5Aclose (attr);
status = H5Dclose (dset);
status = H5Dclose (dset2);
status = H5Sclose (space);
status = H5Fclose (file);
/*
* Now we begin the read section of this example. Here we assume
* the attribute has the same name and rank, but can have any size.
* Therefore we must allocate a new array to read in data using
* malloc().
*/
/*
* Open file, dataset, and attribute.
*/
file = H5Fopen (FILE, H5F_ACC_RDONLY, H5P_DEFAULT);
dset = H5Dopen (file, DATASET, H5P_DEFAULT);
attr = H5Aopen (dset, ATTRIBUTE, H5P_DEFAULT);
/*
* Get dataspace and allocate memory for read buffer.
*/
space = H5Aget_space (attr);
ndims = H5Sget_simple_extent_dims (space, dims, NULL);
rdata = (hdset_reg_ref_t *) malloc (dims[0] * sizeof (hdset_reg_ref_t));
status = H5Sclose (space);
/*
* Read the data.
*/
status = H5Aread (attr, H5T_STD_REF_DSETREG, rdata);
/*
* Output the data to the screen.
*/
for (i=0; i<dims[0]; i++) {
printf ("%s[%d]:\n ->", ATTRIBUTE, i);
/*
* Open the referenced object, retrieve its region as a
* dataspace selection.
*/
dset2 = H5Rdereference (dset, H5P_DEFAULT, H5R_DATASET_REGION, &rdata[i]);
space = H5Rget_region (dset, H5R_DATASET_REGION, &rdata[i]);
/*
* Get the length of the object's name, allocate space, then
* retrieve the name.
*/
size = 1 + H5Iget_name (dset2, NULL, 0);
name = (char *) malloc (size);
size = H5Iget_name (dset2, name, size);
/*
* Allocate space for the read buffer. We will only allocate
* enough space for the selection, plus a null terminator. The
* read buffer will be 1-dimensional.
*/
npoints = H5Sget_select_npoints (space);
rdata2 = (char *) malloc (npoints + 1);
/*
* Read the dataset region, and add a null terminator so we can
* print it as a string.
*/
memspace = H5Screate_simple (1, (hsize_t *) &npoints, NULL);
status = H5Dread (dset2, H5T_NATIVE_CHAR, memspace, space, H5P_DEFAULT,
rdata2);
rdata2[npoints] = '\0';
/*
* Print the name and region data, close and release resources.
*/
printf (" %s: %s\n", name, rdata2);
free (rdata2);
free (name);
status = H5Sclose (space);
status = H5Sclose (memspace);
status = H5Dclose (dset2);
}
/*
* Close and release resources.
*/
free (rdata);
status = H5Aclose (attr);
status = H5Dclose (dset);
status = H5Fclose (file);
return 0;
}
ObjectReference Object::reference () const {
ObjectReference ref;
Exception::check ("H5Rcreate", H5Rcreate (&ref.value (), handle (), ".", H5R_OBJECT, -1));
return ref;
}
int do_copy_refobjs(hid_t fidin,
hid_t fidout,
trav_table_t *travt,
pack_opt_t *options) /* repack options */
{
hid_t grp_in=(-1); /* read group ID */
hid_t grp_out=(-1); /* write group ID */
hid_t dset_in=(-1); /* read dataset ID */
hid_t dset_out=(-1); /* write dataset ID */
hid_t type_in=(-1); /* named type ID */
hid_t dcpl_id=(-1); /* dataset creation property list ID */
hid_t space_id=(-1); /* space ID */
hid_t ftype_id=(-1); /* file data type ID */
hid_t mtype_id=(-1); /* memory data type ID */
size_t msize; /* memory size of memory type */
hsize_t nelmts; /* number of elements in dataset */
int rank; /* rank of dataset */
hsize_t dims[H5S_MAX_RANK]; /* dimensions of dataset */
unsigned int i, j;
int k;
/*-------------------------------------------------------------------------
* browse
*-------------------------------------------------------------------------
*/
for ( i = 0; i < travt->nobjs; i++)
{
switch ( travt->objs[i].type )
{
/*-------------------------------------------------------------------------
* H5G_GROUP
*-------------------------------------------------------------------------
*/
case H5G_GROUP:
/*-------------------------------------------------------------------------
* copy referenced objects in attributes
*-------------------------------------------------------------------------
*/
if ((grp_out=H5Gopen(fidout,travt->objs[i].name))<0)
goto error;
if((grp_in = H5Gopen (fidin,travt->objs[i].name))<0)
goto error;
if (copy_refs_attr(grp_in,grp_out,options,travt,fidout)<0)
goto error;
if (H5Gclose(grp_out)<0)
goto error;
if (H5Gclose(grp_in)<0)
goto error;
/*-------------------------------------------------------------------------
* check for hard links
*-------------------------------------------------------------------------
*/
if (travt->objs[i].nlinks)
{
for ( j=0; j<travt->objs[i].nlinks; j++)
{
H5Glink(fidout,
H5G_LINK_HARD,
travt->objs[i].name,
travt->objs[i].links[j].new_name);
}
}
break;
/*-------------------------------------------------------------------------
* H5G_DATASET
*-------------------------------------------------------------------------
*/
case H5G_DATASET:
if ((dset_in=H5Dopen(fidin,travt->objs[i].name))<0)
goto error;
if ((space_id=H5Dget_space(dset_in))<0)
goto error;
if ((ftype_id=H5Dget_type (dset_in))<0)
goto error;
if ((dcpl_id=H5Dget_create_plist(dset_in))<0)
goto error;
if ( (rank=H5Sget_simple_extent_ndims(space_id))<0)
goto error;
if ( H5Sget_simple_extent_dims(space_id,dims,NULL)<0)
goto error;
nelmts=1;
for (k=0; k<rank; k++)
nelmts*=dims[k];
if ((mtype_id=h5tools_get_native_type(ftype_id))<0)
goto error;
if ((msize=H5Tget_size(mtype_id))==0)
goto error;
/*-------------------------------------------------------------------------
* check if the dataset creation property list has filters that
* are not registered in the current configuration
* 1) the external filters GZIP and SZIP might not be available
* 2) the internal filters might be turned off
*-------------------------------------------------------------------------
*/
if (h5tools_canreadf((NULL),dcpl_id)==1)
{
/*-------------------------------------------------------------------------
* test for a valid output dataset
*-------------------------------------------------------------------------
*/
dset_out = FAIL;
/*-------------------------------------------------------------------------
* object references are a special case
* we cannot just copy the buffers, but instead we recreate the reference
*-------------------------------------------------------------------------
*/
if (H5Tequal(mtype_id, H5T_STD_REF_OBJ))
{
H5G_obj_t1 obj_type;
hid_t refobj_id;
hobj_ref_t *refbuf=NULL; /* buffer for object references */
hobj_ref_t *buf=NULL;
const char* refname;
unsigned u;
/*-------------------------------------------------------------------------
* read to memory
*-------------------------------------------------------------------------
*/
if (nelmts)
{
buf=(void *) HDmalloc((unsigned)(nelmts*msize));
if ( buf==NULL){
printf( "cannot read into memory\n" );
goto error;
}
if (H5Dread(dset_in,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
goto error;
if ((obj_type = H5Rget_obj_type(dset_in,H5R_OBJECT,buf))<0)
goto error;
refbuf=HDcalloc((unsigned)nelmts,msize);
if ( refbuf==NULL){
printf( "cannot allocate memory\n" );
goto error;
}
for ( u=0; u<nelmts; u++)
{
H5E_BEGIN_TRY {
if ((refobj_id = H5Rdereference(dset_in,H5R_OBJECT,&buf[u]))<0)
continue;
} H5E_END_TRY;
/* get the name. a valid name could only occur in the
second traversal of the file */
if ((refname=MapIdToName(refobj_id,travt))!=NULL)
{
/* create the reference, -1 parameter for objects */
if (H5Rcreate(&refbuf[u],fidout,refname,H5R_OBJECT,-1)<0)
goto error;
if(options->verbose)
{
printf(FORMAT_OBJ,"dset",travt->objs[i].name );
printf("object <%s> object reference created to <%s>\n",
travt->objs[i].name,
refname);
}
}/*refname*/
close_obj(obj_type,refobj_id);
}/* u */
}/*nelmts*/
/*-------------------------------------------------------------------------
* create/write dataset/close
*-------------------------------------------------------------------------
*/
if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,mtype_id,space_id,dcpl_id))<0)
goto error;
if (nelmts) {
if (H5Dwrite(dset_out,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,refbuf)<0)
goto error;
}
if (buf)
free(buf);
if (refbuf)
free(refbuf);
}/*H5T_STD_REF_OBJ*/
/*-------------------------------------------------------------------------
* dataset region references
*-------------------------------------------------------------------------
*/
else if (H5Tequal(mtype_id, H5T_STD_REF_DSETREG))
{
H5G_obj_t1 obj_type;
hid_t refobj_id;
hdset_reg_ref_t *refbuf=NULL; /* input buffer for region references */
hdset_reg_ref_t *buf=NULL; /* output buffer */
const char* refname;
unsigned u;
/*-------------------------------------------------------------------------
* read input to memory
*-------------------------------------------------------------------------
*/
if (nelmts)
{
buf=(void *) HDmalloc((unsigned)(nelmts*msize));
if ( buf==NULL){
printf( "cannot read into memory\n" );
goto error;
}
if (H5Dread(dset_in,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
goto error;
if ((obj_type = H5Rget_obj_type(dset_in,H5R_DATASET_REGION,buf))<0)
goto error;
/*-------------------------------------------------------------------------
* create output
*-------------------------------------------------------------------------
*/
refbuf=HDcalloc(sizeof(hdset_reg_ref_t),(size_t)nelmts); /*init to zero */
if ( refbuf==NULL){
printf( "cannot allocate memory\n" );
goto error;
}
for ( u=0; u<nelmts; u++)
{
H5E_BEGIN_TRY {
if ((refobj_id = H5Rdereference(dset_in,H5R_DATASET_REGION,&buf[u]))<0)
continue;
} H5E_END_TRY;
/* get the name. a valid name could only occur in the
second traversal of the file */
if ((refname=MapIdToName(refobj_id,travt))!=NULL)
{
hid_t region_id; /* region id of the referenced dataset */
if ((region_id = H5Rget_region(dset_in,H5R_DATASET_REGION,&buf[u]))<0)
goto error;
/* create the reference, we need the space_id */
if (H5Rcreate(&refbuf[u],fidout,refname,H5R_DATASET_REGION,region_id)<0)
goto error;
if (H5Sclose(region_id)<0)
goto error;
if(options->verbose)
{
printf(FORMAT_OBJ,"dset",travt->objs[i].name );
printf("object <%s> region reference created to <%s>\n",
travt->objs[i].name,
refname);
}
}/*refname*/
close_obj(obj_type,refobj_id);
}/* u */
}/*nelmts*/
/*-------------------------------------------------------------------------
* create/write dataset/close
*-------------------------------------------------------------------------
*/
if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,mtype_id,space_id,dcpl_id))<0)
goto error;
if (nelmts) {
if (H5Dwrite(dset_out,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,refbuf)<0)
goto error;
}
if (buf)
free(buf);
if (refbuf)
free(refbuf);
} /* H5T_STD_REF_DSETREG */
/*-------------------------------------------------------------------------
* not references, open previously created object in 1st traversal
*-------------------------------------------------------------------------
*/
else
{
if ((dset_out=H5Dopen(fidout,travt->objs[i].name))<0)
goto error;
}
assert(dset_out!=FAIL);
/*-------------------------------------------------------------------------
* copy referenced objects in attributes
*-------------------------------------------------------------------------
*/
if (copy_refs_attr(dset_in,dset_out,options,travt,fidout)<0)
goto error;
/*-------------------------------------------------------------------------
* check for hard links
*-------------------------------------------------------------------------
*/
if (travt->objs[i].nlinks)
{
for ( j=0; j<travt->objs[i].nlinks; j++){
H5Glink(fidout,
H5G_LINK_HARD,
travt->objs[i].name,
travt->objs[i].links[j].new_name);
}
}
if (H5Dclose(dset_out)<0)
goto error;
}/*can_read*/
/*
* test_objnames
* Tests that UTF-8 can be used for object names in the file.
* Tests groups, datasets, named datatypes, and soft links.
* Note that this test doesn't actually mark the names as being
* in UTF-8. At the time this test was written, that feature
* didn't exist in HDF5, and when the character encoding property
* was added to links it didn't change how they were stored in the file,
* -JML 2/2/2006
*/
void test_objnames(hid_t fid, const char* string)
{
hid_t grp_id, grp1_id, grp2_id, grp3_id;
hid_t type_id, dset_id, space_id;
char read_buf[MAX_STRING_LENGTH];
char path_buf[MAX_PATH_LENGTH];
hsize_t dims=1;
hobj_ref_t obj_ref;
herr_t ret;
/* Create a group with a UTF-8 name */
grp_id = H5Gcreate2(fid, string, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
CHECK(grp_id, FAIL, "H5Gcreate2");
/* Set a comment on the group to test that we can access the group
* Also test that UTF-8 comments can be read.
*/
ret = H5Oset_comment_by_name(fid, string, string, H5P_DEFAULT);
CHECK(ret, FAIL, "H5Oset_comment_by_name");
ret = H5Oget_comment_by_name(fid, string, read_buf, (size_t)MAX_STRING_LENGTH, H5P_DEFAULT);
CHECK(ret, FAIL, "H5Oget_comment_by_name");
ret = H5Gclose(grp_id);
CHECK(ret, FAIL, "H5Gclose");
VERIFY(HDstrcmp(string, read_buf), 0, "strcmp");
/* Create a new dataset with a UTF-8 name */
grp1_id = H5Gcreate2(fid, GROUP1_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
CHECK(grp1_id, FAIL, "H5Gcreate2");
space_id = H5Screate_simple(RANK, &dims, NULL);
CHECK(space_id, FAIL, "H5Screate_simple");
dset_id = H5Dcreate2(grp1_id, string, H5T_NATIVE_INT, space_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
CHECK(dset_id, FAIL, "H5Dcreate2");
/* Make sure that dataset can be opened again */
ret = H5Dclose(dset_id);
CHECK(ret, FAIL, "H5Dclose");
ret = H5Sclose(space_id);
CHECK(ret, FAIL, "H5Sclose");
dset_id = H5Dopen2(grp1_id, string, H5P_DEFAULT);
CHECK(ret, FAIL, "H5Dopen2");
ret = H5Dclose(dset_id);
CHECK(ret, FAIL, "H5Dclose");
ret = H5Gclose(grp1_id);
CHECK(ret, FAIL, "H5Gclose");
/* Do the same for a named datatype */
grp2_id = H5Gcreate2(fid, GROUP2_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
CHECK(grp2_id, FAIL, "H5Gcreate2");
type_id = H5Tcreate(H5T_OPAQUE, (size_t)1);
CHECK(type_id, FAIL, "H5Tcreate");
ret = H5Tcommit2(grp2_id, string, type_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
CHECK(type_id, FAIL, "H5Tcommit2");
ret = H5Tclose(type_id);
CHECK(type_id, FAIL, "H5Tclose");
type_id = H5Topen2(grp2_id, string, H5P_DEFAULT);
CHECK(type_id, FAIL, "H5Topen2");
ret = H5Tclose(type_id);
CHECK(type_id, FAIL, "H5Tclose");
/* Don't close the group -- use it to test that object references
* can refer to objects named in UTF-8 */
space_id = H5Screate_simple(RANK, &dims, NULL);
CHECK(space_id, FAIL, "H5Screate_simple");
dset_id = H5Dcreate2(grp2_id, DSET3_NAME, H5T_STD_REF_OBJ, space_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
CHECK(ret, FAIL, "H5Dcreate2");
/* Create reference to named datatype */
ret = H5Rcreate(&obj_ref, grp2_id, string, H5R_OBJECT, -1);
CHECK(ret, FAIL, "H5Rcreate");
/* Write selection and read it back*/
ret = H5Dwrite(dset_id, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, &obj_ref);
CHECK(ret, FAIL, "H5Dwrite");
ret = H5Dread(dset_id, H5T_STD_REF_OBJ, H5S_ALL, H5S_ALL, H5P_DEFAULT, &obj_ref);
CHECK(ret, FAIL, "H5Dread");
/* Ensure that we can open named datatype using object reference */
type_id = H5Rdereference2(dset_id, H5P_DEFAULT, H5R_OBJECT, &obj_ref);
CHECK(type_id, FAIL, "H5Rdereference2");
ret = H5Tcommitted(type_id);
VERIFY(ret, 1, "H5Tcommitted");
ret = H5Tclose(type_id);
CHECK(type_id, FAIL, "H5Tclose");
ret = H5Dclose(dset_id);
CHECK(ret, FAIL, "H5Dclose");
ret = H5Sclose(space_id);
CHECK(ret, FAIL, "H5Sclose");
ret = H5Gclose(grp2_id);
CHECK(ret, FAIL, "H5Gclose");
/* Create "group3". Build a hard link from group3 to group2, which has
* a datatype with the UTF-8 name. Create a soft link in group3
* pointing through the hard link to the datatype. Give the soft
* link a name in UTF-8. Ensure that the soft link works. */
grp3_id = H5Gcreate2(fid, GROUP3_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
CHECK(grp3_id, FAIL, "H5Gcreate2");
ret = H5Lcreate_hard(fid, GROUP2_NAME, grp3_id, GROUP2_NAME, H5P_DEFAULT, H5P_DEFAULT);
CHECK(ret, FAIL, "H5Lcreate_hard");
HDstrcpy(path_buf, GROUP2_NAME);
HDstrcat(path_buf, "/");
HDstrcat(path_buf, string);
ret = H5Lcreate_hard(grp3_id, path_buf, H5L_SAME_LOC, string, H5P_DEFAULT, H5P_DEFAULT);
CHECK(ret, FAIL, "H5Lcreate_hard");
/* Open named datatype using soft link */
type_id = H5Topen2(grp3_id, string, H5P_DEFAULT);
CHECK(type_id, FAIL, "H5Topen2");
ret = H5Tclose(type_id);
CHECK(type_id, FAIL, "H5Tclose");
ret = H5Gclose(grp3_id);
CHECK(ret, FAIL, "H5Gclose");
}